A major goal of this research is to understand the complex interplay between transcription factors and epigenomic modification that regulates gene expression programs establishing and maintaining adipocyte cells. We recently identified the glucocorticoid receptor (GR) and CAAT/enhancer binding protein (CEBP) as critical transcriptional regulators that activate the adipogenic program by co occupying thousands of specific sites in the genome during early adipogenesis. We hypothesize that GRCEBPbound regions, the majority of which are positioned far away from active genes, control transcription by forming long-range associations with core promoter elements occupied by the transcription initiation apparatus. Specific Aim 1 will identify GR and CEBP direct gene targets and determinants of long-range chromatin interactions on a genome wide scale during mouse adipocyte cell differentiation. Preliminary results from chromatin interaction analysis by paired end tag sequencing (ChIAPET) demonstrate the feasibility of detecting long-range associations for CEBP that globally link distal binding sites with regulated genes. Chromatin conformation capture (3C) validates a loop spanning 170 kilobases of DNA, suggesting that the ChIAPET data are robust and informative. Determinants of DNA looping will be examined by gain and loss of function studies targeting sequence specific factors and coregulator activities. Specific Aim 2 will identify on a genome wide scale the GR and CEBP adipogenic targets that are conserved between human and mouse. Preliminary chromatin immunoprecipitation sequencing (ChIPseq) results reveal that only a small minority of bound sites is shared in both species, and we hypothesize that comparison of the GR and CEBP chromatin interactomes in human and mouse will uncover the direct transcriptional pathways driving adipocyte differentiation. This will be tested by performing ChIAPET for GR and CEBP during adipocyte differentiation of human mesenchymal stem cells (hMSCs). Specific Aim 3 will identify GR and CEBP direct gene targets on a genomewide scale in mouse adipose and liver tissues. Preliminary ChIPseq results reveal extensive colocalization of GR and CEBP in either adipose or liver, but only a minority of bound sites is shared in both tissues. We predict that comparison of the chromatin interactomes from adipose and liver tissues will reveal fundamental mechanisms controlling cell type specific gene expression by GR and CEBP in vivo. As a whole, these studies use an innovative approach that will increase understanding of the development and function of adipose tissue, which normally benefits health, yet in excess as in obesity, is a strong risk for metabolic diseases including diabetes, hyperlipidemia, hypertension and heart disease.